hts_alignment_emitter.hpp File Reference

#include <mutex>
#include <thread>
#include <vector>
#include <deque>
#include <htslib/hfile.h>
#include <htslib/hts.h>
#include <htslib/sam.h>
#include <vg/vg.pb.h>
#include <vg/io/protobuf_emitter.hpp>
#include <vg/io/stream_multiplexer.hpp>
#include "handle.hpp"
#include "vg/io/alignment_emitter.hpp"

Classes
struct	vg::SequenceDictionaryEntry
class	vg::HTSWriter
class	vg::HTSAlignmentEmitter
class	vg::SplicedHTSAlignmentEmitter

Namespaces
	vg

Typedefs
using	vg::SequenceDictionary = std::vector< SequenceDictionaryEntry >

Enumerations
enum	vg::alignment_emitter_flags_t {   vg::ALIGNMENT_EMITTER_FLAG_NONE = 0, vg::ALIGNMENT_EMITTER_FLAG_HTS_RAW = 1, vg::ALIGNMENT_EMITTER_FLAG_HTS_SPLICED = 2, vg::ALIGNMENT_EMITTER_FLAG_HTS_PRUNE_SUSPICIOUS_ANCHORS = 4,   vg::ALIGNMENT_EMITTER_FLAG_VG_USE_SEGMENT_NAMES = 8, vg::ALIGNMENT_EMITTER_FLAG_HTS_ADD_GRAPH_ALIGNMENT_TAG = 16, vg::ALIGNMENT_EMITTER_FLAG_HTS_SUPPLEMENTARY = 32 }

Functions
unique_ptr< AlignmentEmitter >	vg::get_alignment_emitter (const string &filename, const string &format, const SequenceDictionary &paths, size_t max_threads, const HandleGraph *graph, int flags)
SequenceDictionary	vg::get_sequence_dictionary (const string &filename, const vector< string > &path_names, const std::unordered_set< std::string > &reference_samples, const PathPositionHandleGraph &graph)
std::unordered_map< string, size_t >	vg::index_sequence_dictionary (const SequenceDictionary &paths)

Detailed Description

Defines a system for emitting alignments and groups of alignments in multiple formats.